DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes

EcoP15I is a type III restriction enzyme that requires two recognition sites in a defined orientation separated by up to 3.5 kbp to efficiently cleave DNA. The mechanism through which site- bound EcoP15I enzymes communicate between the two sites is unclear. Here, we use atomic force microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number and size distribution of loops formed, we conclude that the loops observed do not result from translocation, but are instead formed by a contact between site- bound EcoP15I and a nonspecific region of DNA. This conclusion is confirmed by a theoretical polymer model. It is further shown that translocation must play some role, because when translocation is blocked by a Lac repressor protein, DNA cleavage is similarly blocked. On the basis of these results, we present a model for restriction by type III restriction enzymes and highlight the similarities between this and other classes of restriction enzymes.

Self-acylation properties of type II fatty acid biosynthesis acyl carrier protein

Acyl carrier protein (ACIP) plays a central role in many metabolic processes inside the cell, and almost 4% of the total enzymes inside the cell require it as a cofactor. Here, we report self-acylation properties in ACPs from Plasmodium falciparum and Brassica napus that are essential components of type II fatty acid biosynthesis (FAS II), disproving the existing notion that this phenomenon is restricted only to ACPs involved in polyketide biosynthesis. We also provide strong evidence to suggest that catalytic self-acylation is intrinsic to the individual ACP. Mutational analysis of these ACPs revealed the key residue(s) involved in this phenomenon. We also demonstrate that these FAS 11 ACPs exhibit a high degree of selectivity for self-acylation employing only dicarboxylic acids as substrates. A plausible mechanism for the self-acylation reaction is also proposed.

Metabolic enzymes as potential drug targets in Plasmodium falciparum.

Plasmodium falciparum causes the most severe form of malaria that is fatal in many cases. Emergence of drug resistant strains of P. falciparum requires that new drug targets be-identified. This review considers in detail enzymes of the glycolytic pathway, purine salvage pathway, pyrimidine biosynthesis and proteases involved in catabolism of haemoglobin. Structural features of P. falciparum triosephosphate isomerase which could be exploited for parasite specific drug development have been highlighted. Utility of P. falciparum hypoxanthine-guanine-phosphoribosyltransferase, adenylosuccinate synthase, dihydroorotate dehydrogenase, thymidylate synthase-dihydrofolate reductase, cysteine and aspartic proteases have been elaborated in detail. The review also briefly touches upon other potential targets in P. falciparum

How pantothenol intervenes in Coenzyme-A biosynthesis of Mycobacterium tuberculosis

Coenzyme A is an indispensable cofactor for all organisms and holds a central position in a number of pathways. Prokaryotic enzymes involved in the synthesis of CoA are quite different from their mammalian counterparts; hence, they are good targets for the development of antimicrobials to treat many diseases. There are antimicrobials that act by inhibiting CoA biosynthesis. It has been suggested that pantothenol exhibits antibacterial activity by competitively inhibiting pantothenate kinase, a key regulatory enzyme for CoA synthesis. Contrary to these suggestions, in this paper, we demonstrate that pantothenol acts as a substrate for Mycobacterium tuberculosis and Escherichia coli pantothenate kinases. The product, 4'-phosphopantothenol, thus formed inhibits competitively the utilization of 4'-phosphopantothenate by CoaBC. Thus, it is the failure of CoaBC to utilize 4'-phosphopantothenol as a substrate that accounts for the bactericidal activity of pantothenol. (C) 2007 Elsevier Inc. All rights reserved.

Biosynthesis of sulfated mucopolysaccharides in relation to vitamins A and K

1.(1) Incorporation of Na235SO4 into acid mucopolysaccharides of intestine and colon tissue has been studied in normal, vitamin A-deficient and excess vitamin A-fed rats. 2. (2) Vitamin A deficiency resulted in a significant decrease in [35S]sulfate incorporation into mucopolysaccharides isolated from intestines of male rats. There was no significant change in the total mucopolysaccharides per gram of fresh tissue. 3. (3) When rats are fed excessive amounts of retinyl acetate, increased [35S]sulfate incorporation into mucopolysaccharides of rat intestine and colon is observed. 4. (4) Supplementation of vitamin K1 to rats fed excessive amounts of vitamin A restores the incorporation of [35S]sulfate into the acid mucopolysaccharides to the normal level. 5. (5) The implications of these findings with special reference to the role of vitamins A and K in the synthesis of sulfated mucopolysaccharides are discussed.

Biosynthesis of ubiquinone and ubichromenol in vitamin A-deficient rats

1. The concentrations of ubiquinone and ubichromenol increased in the livers, but not in the intestines and kidneys, of rats maintained on a diet deficient in vitamin 2. After short time intervals (e.g. 2 h) following administration of the tracer, incorporation of [2-14C]mevalonate into ubiquinone and ubichromenol in livers of vitamin A-deficient rats was lower than for normal animals; this was in contrast to later times (e.g. 72 h) when it was higher. 3. The “newly synthesized” ubiquinone in livers of vitamin A-deficient rats was distributed in all the cell fractions without specific localization. 4. Absorbed exogenous [14C]ubiquinone and [14C]ubichromenol were retained in the livers of vitamin A-deficient rats to a larger extent and for a longer time than in the normal animals. 5. The results suggest that the accumulation of ubiquinone and ubichromenol in the livers of vitamin A-deficient rats is due to lowered catabolism and not to increased rate of synthesis.

Biosynthesis of valine and isoleucine in plants II. Dihydroxyacid dehydratase from Phaseolus radiatus

1. 1. An enzyme catalysing the conversion of α,β-dihydroxyisovalerate and α,β-dihydroxy-β-methylvalerate to α-ketoisovalerate and α-keto-β-methylvalerate has been partially purified from green gram (Phaseolus radiatus), and its characteristics studied. 2. 2. A natural inhibitor, heat stable and inorganic in nature, was observed in the crude extracts. 3. 3. The observed Km values for α-β-dihydroxyisovalerate and α,β-dihydroxy-β-methylvalerate were 2.4 · 10-3 M and 9 · 10-4 M, respectively. 4. 4. The enzyme required the presence of a divalent metal ion (Mg2+, Mn2+ or Fe2+) for maximal activity. Heavy metals like Ag+ and Hg2+ were inhibitory. 5. 5. The optimal activity was around pH 8.0 and the optimum temperature at 52°. The activation energy is found to be 12 600 cal/mole. 6. 6. The enzyme was inhibited by p-hydroxymercuribenzoate, N-ethylmaleimide and sulphydryl compounds like cysteine, glutathione, 2-mercaptoethanol and 2,3-dimercaptopropanol. The inhibition by p-hydroxymercuribenzoate could not be reversed by any of the sulfhydryl compounds tested.

Studies of the enzymes involved in nicotinamide adenine dinucleotide metabolism in Aspergillus niger

The enzyme nicotinamide amidase (nicotinamide amidohydrolase) was purified 57-fold from Aspergillus niger. The purified preparation was specific towards its substrate nicotinamide and did not deamidate NADP, NAD, NMN, N′-methyl nicotinamide, asparagine, glutamine, benzamide, α-naphthaleneamide and indoleacetamide. The asparagine, glutamine, benzamide, α-naphthaleneamide and indoleacetamide.vThe optimum pH was found to be 7.5. Temperature optimum was 40°. It had a Km value of 6.504 · 10−4 M towards nicotinamide. The enzyme exhibited Mg2+ ion requirement for its optimum activity. NAD-glycohydrolase (EC 3.2.2.5) was purified 109-fold from the mold. A. niger. The enzyme preparation was active only towards NAD and NADP and did not attack NMN, N′-methylnicotinamide and NADH. The Km value for NAD was found to be 7.693 · 10−6 M. The enzyme did not require any metal ion for its activity. It is suggested that A. niger will serve a better source for a large scale preparation of NAD-glycohydrolase than the Neurospora mold. The biological role of both NAD-glycohydrolase and nicotinamide amidase in the regulation of cellular NAD level has been discussed. It is, further, observed that NAD did not exert its feedback control on nicotinamide amidase at least in A. niger.

Biosynthesis of valine and isoleucine in plants I. Formation of α-acetolactate in Phaseolus radiatus

1. 1. The presence of an enzyme system in plants catalyzing the formation of α-acetolactate from pyruvate has been demonstrated; the system in green gram (Phaseolus radiatus) has been partially purified and its characteristics have been studied.2. Free acetaldehyde is formed as a product of the reaction and so the reaction is mainly diverted towards the formation of acetoin. 3. The system requires thiamine pyrophosphate and a divalent metal ion (Mn2+ or Mg2+) for maximum activity. The optimum pH is around 6.0 and the optimum temperature is 60°. 4. The system is very labile in absence of pyruvate, Mn2+ and DPT. 5. The Km values for pyruvate, Mn2+, Mg2+ and DPT are 3·10−2 M. 5·10−5 M, 2·10−5 M, and e·10−6 M respectively. The activation energy is 3540 cal/mole. 6. The enzyme is strongly inhibited by p-chloromercuribenzoate and the inhibition can be reversed partially by 2-mercaptoethanol, BAL or cysteine. Heavy metals, such as Hg2+ and Ag+, are inhibitory but l-valine does not inhibit the reaction.

Biosynthesis of β-N-oxalyl-l-α,β-diaminopropionic acid, the lathyrus sativus neurotoxin

The biosynthesis of β-N-oxalyl-l-α,β-diaminopropionic acid (ODAP) the Lathyrus sativus neurotoxin has been found to follow the scheme depicted below: {A figure is presented}. The first reaction is catalysed by oxalyl-CoA synthetase which has properties similar to that of the enzyme in peas. The second reaction is catalysed by another enzyme which is specific to L. sativus and is designated as oxalyl-CoA-α,β-diaminopropionic acid oxalyl transferase. The enzymes have been purified by about 60-fold and their properties studied. A partial resolution of the two enzyme activities has been achieved using CM-sephadex columns.